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moshi4 / pyMSAviz

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
https://moshi4.github.io/pyMSAviz
MIT License
80 stars 14 forks source link

Visualizing only a subset of the sequences #13

Closed StefanoLonardi closed 3 months ago

StefanoLonardi commented 3 months ago

Many thanks for your great tool. I am trying to visualize the alignment between a LOT of proteins (almost 200), and it takes an enormous amount of space. I am trying to figure out how to visualize only a subset. I know I can remove some of the sequences from the alignment using Biophython, but the consensus produces by pyMSAviz would not be accurate. Is there any way to specify a subset of the input sequences to be visualized? Thanks in advance, Stefano

moshi4 commented 3 months ago

Hi @StefanoLonardi,

As you commented above, visualization of the subset MSA would be possible by extracting the subset from the overall MSA using BioPython. If you want to add the consensus of the overall MSA with the visualization of the subset MSA, unfortunately, pyMSAviz does not have the functionality to fulfill your request. I have no plans to add that functionality as well.